Bioinformatics Ex

What is bioinformatics?

The use of computational tools to analyze biological data.

Why is bioinformatics needed?

Sequencing produces huge amounts of data that must be analyzed.

What is a genome?

The complete genetic information of an organism.

What is genome annotation?

Describing DNA sequences and identifying their important features.

What can genome size tell us?

It can provide useful information about an organism.

What is Sanger sequencing?

A first-generation method that reads DNA using fluorescent signals.

When was Sanger sequencing developed?

The 1970s.

What is next-generation sequencing (NGS)?

A high-throughput method that sequences massive amounts of DNA in parallel.

What type of sequences does NGS use?

Short-read sequences.

What is Illumina sequencing?

A widely used NGS technology.

What is long-read sequencing?

Sequencing technology that produces much longer DNA reads.

How does nanopore sequencing work?

DNA passes through a pore and nucleotide-dependent electrical signals are measured.

What is metagenomics?

Sequencing and analyzing all DNA sequences in an environment.

What is environmental DNA (eDNA)?

DNA collected from an environmental sample.

What can eDNA be used to track?

Species, invasive organisms, and environmental quality.

How can bioinformatics help medical research?

It can identify genetic links to diseases and mutations.

Why is cancer especially relevant to genomic research?

Cancer often arises from mutations.

What is paleogenomics?

The sequencing and analysis of ancient DNA.

What can paleogenomics reveal?

Information about extinct species and evolutionary history.

Why must genomic data be annotated?

To make the DNA sequence biologically useful.

What is a codon?

A three-base sequence in mRNA that specifies an amino acid.

What is an anticodon?

A sequence in tRNA that base-pairs with an mRNA codon.

What determines the amino acid added to a protein?

The mRNA codon sequence.

What is the genetic code?

The rules connecting mRNA codons to amino acids.

What does a start codon do?

It marks where protein translation begins.

What is the common start codon?

ATG.

What are the three stop codons?

TAA, TAG, and TGA.

What is an ORF?

A sequence that can potentially encode a protein.

What are UTRs?

Untranslated regions of a gene transcript.

What are exons?

Gene regions that remain in the mature transcript.

What are introns?

Gene regions removed during RNA processing.

What is sequence alignment?

Comparing DNA or protein sequences to identify similarities.

What is pairwise alignment?

Comparing two sequences directly.

What is multiple sequence alignment?

Comparing multiple sequences at the same time.

What can sequence alignment help determine?

The effects of mutations and evolutionary relationships.

What is the Genographic Project?

A project using comparative mitochondrial DNA to study human evolution.

What is a database?

A repository of electronic information.

What is NCBI?

A collection of biological databases organized by the National Library of Medicine.

What is Entrez?

A system used to search and retrieve information from NCBI databases.

What does the AND search operator do?

Requires both search terms.

What does the OR search operator do?

Includes either search term.

What does the NOT search operator do?

Excludes the term following NOT.

What is an accession ID?

A unique identifier given to an entry in an NCBI database.

What is the Nucleotide Database used for?

Finding DNA sequences and related information.

What is FASTA?

A standard text format for storing sequence data.

What does a FASTA file contain?

A header line followed by the sequence.

What is GenBank?

A database/record format containing sequence and related information.

How does FASTA differ from GenBank?

FASTA focuses on the sequence; GenBank contains sequence plus additional information.

What information can an NCBI gene page contain?

Gene ID, organism, gene type, transcripts, proteins, and publications.

What genome information can an NCBI gene page contain?

Genome assembly, accession ID, chromosome, and genomic location.

What is PubMed?

A database for searching scientific journal literature.

What are PubMed filters used for?

Narrowing results by date, availability, article type, and more.

What is PubMed Central (PMC)?

A database containing free-to-read or open-access articles.

What is OMIM?

Online Mendelian Inheritance in Man.

What is OMIM useful for?

Finding information about human genetic diseases and variants.

What is NCBI Taxonomy?

A database for taxonomic information about organisms.

What can the NCBI Taxonomy Browser show?

Taxonomic rank, scientific name, common name, genetic code, genome information, and lineage.

Why is taxonomy important in bioinformatics?

It helps identify the organism associated with sequence data.

What is UniProt?

A resource providing protein information.

What is UniProtKB?

The UniProt Knowledge Base.

What information can UniProt provide?

Protein information such as subcellular location, structure, and isoforms.

Why look at protein information?

Proteins are the functional units of cells.

What is the basic flow of genetic information?

DNA → RNA → protein.

What is an isoform?

A different form of a protein produced from the same gene.

What is the Protein Data Bank (PDB)?

A database of experimentally determined protein structures.

What does RCSB PDB stand for?

Research Collaboratory for Structural Bioinformatics Protein Data Bank.

What can a PDB page contain?

Structure image, PDB ID, protein data, deposition data, and experimental data.

Why use filters in PDB?

To find the desired organism or structure.

What is KEGG?

A database containing biological pathways and functional information.

What is KEGG Orthology (KO)?

A database that summarizes information for functional orthologs.

What is a functional ortholog?

Proteins from different organisms that accomplish the same function.

What can KEGG pathways show?

How genes and proteins participate in biological pathways.

What are the three major functional databases covered?

UniProt, PDB, and KEGG.

What is a major limitation of UniProt?

It focuses on protein data.

What is a major limitation of PDB?

It contains experimentally defined structures.

What is a major limitation of KEGG?

It focuses on well-studied proteins found across multiple organisms.

What is BLAST?

Basic Local Alignment Search Tool.

What is BLAST used for?

Finding database sequences similar to a query sequence.

What is a query sequence?

The sequence submitted to BLAST.

What is a subject sequence?

A database sequence compared with the query.

What type of alignment does BLAST use?

Local alignment.

What does local alignment mean?

It finds matching regions rather than requiring entire sequences to align.

What is BLASTn?

BLAST used to compare nucleotide sequences.

What is megaBLAST?

A BLASTn approach designed for highly similar nucleotide sequences.

How many nucleotide bases are in a BLASTn word?

11 nucleotides.

How many nucleotide bases are in a megaBLAST word?

28 nucleotides.

What is query cover?

The percentage of the query sequence that aligned to the subject.

What is the ideal query cover?

100%.

What is E-value?

The probability of obtaining an alignment by random chance.

What is the ideal E-value?

Very low, with 0.0 being best.

What is percent identity?

The percentage of aligned positions that are identical.

What is the ideal percent identity?

100%.

What does a higher BLAST score generally indicate?

A better alignment.

What two values should be balanced when evaluating BLAST hits?

Query cover and percent identity.

Why should BLAST results be checked carefully?

Tables, graphical summaries, and alignments provide complementary information.

What does a BLAST alignment show?

Matches and mismatches between query and subject.

What is a homolog?

A sequence sharing similarity due to common ancestry.

What is an ortholog?

A homolog that arose through a speciation event.

What is a paralog?

A homolog that arose through a gene duplication event.

What is sequence conservation?

High sequence similarity across orthologs.